This HTML document contains the output of CATS-rb transcriptome
assembly comparison tool. For more details on each table and figure,
refer to the tool’s documentation. In order to customize different
plotting parameters, refer to the tool’s documentation.
Table 1. General transcriptome assembly statistics.
| Parameter | d_melanogaster_bdgp6 | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 |
|---|---|---|---|---|---|---|---|
| N transcripts | 35722 | 27748 | 30651 | 36610 | 18601 | 18652 | 19217 |
| Total transcriptome length (bp) | 92747399 | 34167218 | 32433743 | 27462499 | 44994186 | 44145594 | 42094487 |
| GC content (%) | 49.14% | 49.17% | 49.34% | 49.68% | 48.43% | 48.45% | 48.60% |
| N, (%) transcripts with length higher or equal to 200 bp | 34155, (95.61%) | 23903, 86.14% | 25617, 83.58% | 28233, 77.12% | 18277, 98.26% | 18225, 97.71% | 18132, 94.35% |
| N, (%) transcripts with length higher or equal to 500 bp | 32238, (90.25%) | 14553, 52.45% | 13923, 45.42% | 11423, 31.2% | 16878, 90.74% | 16738, 89.74% | 16335, 85% |
| N, (%) transcripts with length higher or equal to 1000 bp | 26475, (74.11%) | 9887, 35.63% | 8846, 28.86% | 6486, 17.72% | 13488, 72.51% | 13356, 71.61% | 12875, 67% |
| N, (%) transcripts with length higher or equal to 5000 bp | 4248, (11.89%) | 1036, 3.73% | 914, 2.98% | 608, 1.66% | 2003, 10.77% | 1931, 10.35% | 1766, 9.19% |
| N, (%) transcripts with length higher or equal to 10000 bp | 620, (1.74%) | 93, 0.34% | 90, 0.29% | 59, 0.16% | 228, 1.23% | 221, 1.18% | 202, 1.05% |
| N, (%) transcripts with length higher or equal to 20000 bp | 61, (0.17%) | 4, 0.01% | 6, 0.02% | 6, 0.02% | 10, 0.05% | 10, 0.05% | 6, 0.03% |
| Mean transcript length (bp) | 2596.37 | 1231.34 | 1058.16 | 750.14 | 2418.91 | 2366.8 | 2190.48 |
| Median trancript length (bp) | 1879 | 547.5 | 434 | 310 | 1756 | 1714 | 1575 |
| Transcript length IQR (bp) | 970-3370 | 258-1570 | 234-1238 | 206-641 | 926-3168 | 899-3096 | 762-2878 |
| Trancript length range (bp) | 18-71382 | 131-60159 | 131-58349 | 131-45657 | 131-50033 | 131-50033 | 131-49970 |
| N50 (bp) | 3836 | 2597 | 2388 | 1831 | 3590 | 3527 | 3401 |
| L50 | 5542 | 3745 | 3737 | 3789 | 3836 | 3816 | 3748 |
| N90 (bp) | 1345 | 477 | 372 | 249 | 1215 | 1194 | 1135 |
| L90 | 26715 | 14985 | 16939 | 22581 | 12212 | 12182 | 12096 |
| Parameter | RSP_0.005_11_20 | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|---|
| N transcripts | 18641 | 18719 | 19432 |
| Total transcriptome length (bp) | 45586004 | 45065633 | 43400943 |
| GC content (%) | 48.37% | 48.39% | 48.52% |
| N, (%) transcripts with length higher or equal to 200 bp | 18371, 98.55% | 18312, 97.83% | 18210, 93.71% |
| N, (%) transcripts with length higher or equal to 500 bp | 17019, 91.3% | 16886, 90.21% | 16573, 85.29% |
| N, (%) transcripts with length higher or equal to 1000 bp | 13620, 73.06% | 13517, 72.21% | 13131, 67.57% |
| N, (%) transcripts with length higher or equal to 5000 bp | 2024, 10.86% | 1987, 10.61% | 1872, 9.63% |
| N, (%) transcripts with length higher or equal to 10000 bp | 234, 1.26% | 230, 1.23% | 225, 1.16% |
| N, (%) transcripts with length higher or equal to 20000 bp | 10, 0.05% | 12, 0.06% | 11, 0.06% |
| Mean transcript length (bp) | 2445.47 | 2407.48 | 2233.48 |
| Median trancript length (bp) | 1778 | 1749 | 1605 |
| Transcript length IQR (bp) | 944-3211 | 914-3153.5 | 776.75-2950 |
| Trancript length range (bp) | 131-50248 | 132-50317 | 132-50173 |
| N50 (bp) | 3602 | 3576 | 3485 |
| L50 | 3876 | 3847 | 3794 |
| N90 (bp) | 1224 | 1214 | 1160 |
| L90 | 12283 | 12234 | 12208 |
IQR = interquartile range
Figure 1. Transcript length distribution.
Table 2. Transcriptome assembly mapping statistics.
| Parameter | d_melanogaster_bdgp6 | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 |
|---|---|---|---|---|---|---|---|
| N, % unmapped transcripts | 499, 1.4% | 7, 0.03% | 2, 0.01% | 4, 0.01% | 3, 0.02% | 2, 0.01% | 4, 0.02% |
| Transcript alignment proportion (mean, IQR) | 1, 1-1 | 0.98, 1-1 | 0.98, 1-1 | 0.97, 1-1 | 0.99, 1-1 | 0.99, 1-1 | 0.99, 1-1 |
| N, % multimapped transcripts | 1029, 2.88% | 136, 0.73% | 216, 0.7% | 188, 0.68% | 152, 0.82% | 153, 0.8% | 147, 0.79% |
| N, % structural inconsistent transcripts | 547, 1.53% | 1622, 5.85% | 1997, 6.52% | 2842, 7.76% | 342, 1.84% | 385, 2.06% | 696, 3.62% |
| N exons | 77321 | 76835 | 72591 | 189645 | 83914 | 84838 | 79302 |
| N exons per transcript (mean, IQR) | 5.38, 2-7 | 2.81, 1-3 | 2.54, 1-3 | 2.08, 1-2 | 4.54, 2-6 | 4.46, 2-6 | 4.26, 2-6 |
| Exon length (bp) (mean, IQR) | 488.33, 145-555 | 427.36, 148-478 | 406.46, 149-450 | 360.03, 150-388 | 528.65, 152-612 | 526.65, 152-610 | 521.59, 152-603 |
| Parameter | RSP_0.005_11_20 | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|---|
| N, % unmapped transcripts | 0, 0.00% | 2, 0.01% | 9, 0.05% |
| Transcript alignment proportion (mean, IQR) | 0.99, 1-1 | 0.99, 1-1 | 0.99, 1-1 |
| N, % multimapped transcripts | 153, 0.82% | 162, 0.83% | 249, 0.68% |
| N, % structural inconsistent transcripts | 301, 1.61% | 390, 2.08% | 511, 2.63% |
| N exons | 81074 | 82706 | 84058 |
| N exons per transcript (mean, IQR) | 4.57, 2-6 | 4.52, 2-6 | 4.37, 2-6 |
| Exon length (bp) (mean, IQR) | 531.14, 153-613 | 529.81, 153-612 | 526.2, 153-610 |
IQR = interquartile range
Figure 2. Transcript alignment proportion category
distribution.
Figure 3. Number of exons per transcript category
distribution.
Figure 4. Exon length distribution.
Table 3. Exon set statistics.
| Parameter | d_melanogaster_bdgp6 | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 |
|---|---|---|---|---|---|---|---|
| N exon sets | 64093 | 63265 | 63560 | 62016 | 60365 | 60271 | 59789 |
| Exon set length (bp) (mean, IQR) | 559.41, 156-652 | 448.88, 153-514 | 425.07, 153-485 | 379.64, 153-421 | 558.64, 160-661 | 556.2, 160-658 | 550.61, 159-651 |
| N, % exon sets included in completeness analyses | 64093, 100% | 63265, 100% | 63560, 100% | 62016, 100% | 60365, 100% | 60271, 100% | 59789, 100% |
| N, % unique exon sets | 2621, 4.09% | 23, 0.04% | 19, 0.03% | 32, 0.05% | 9, 0.01% | 7, 0.01% | 11, 0.02% |
| Unique exon set length (bp) (mean, IQR) | 148.61, 69-152 | 537, 187.5-497 | 339.42, 169-464 | 276.88, 159-299.25 | 757.67, 181-521 | 368.57, 256-537 | 512.36, 158-476.5 |
| N missing exon sets found in any transcriptome assembly | 2635 | 92379 | 107392 | 147822 | 42656 | 45259 | 53532 |
| N missing exon sets found in all other transcriptome assemblies | 65 | 7872 | 12637 | 46703 | 512 | 673 | 1877 |
| Common exon set length (bp) (mean, IQR) | 698.57, 192-858 | 547.82, 175-655 | 514.03, 170-608 | 439.6, 158-504 | 674.74, 189-831 | 671.05, 189-828 | 660.14, 187-815 |
| Relative common exon set length (mean, IQR) | 1, 1-1 | 0.87, 0.79-1 | 0.84, 0.7-1 | 0.76, 0.51-1 | 0.98, 1-1 | 0.97, 1-1 | 0.96, 1-1 |
| Relative exon score | 0.995 | 0.714 | 0.671 | 0.57 | 0.894 | 0.887 | 0.864 |
| N missing exon sets inside transcript sets | 2593 | 41092 | 42522 | 43590 | 26926 | 28032 | 31207 |
| N missing exon sets outside transcript sets | 1 | 5095 | 7985 | 20138 | 357 | 453 | 909 |
| Parameter | RSP_0.005_11_20 | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|---|
| N exon sets | 60434 | 60320 | 60019 |
| Exon set length (bp) (mean, IQR) | 561.05, 161-663 | 559.62, 160-661 | 555.66, 160-658 |
| N, % exon sets included in completeness analyses | 60434, 100% | 60320, 100% | 60019, 100% |
| N, % unique exon sets | 8, 0.01% | 3, 0% | 22, 0.04% |
| Unique exon set length (bp) (mean, IQR) | 1503.38, 355-1313.75 | 188.67, 112.5-248.5 | 684.45, 170-529.5 |
| N missing exon sets found in any transcriptome assembly | 40918 | 43055 | 48555 |
| N missing exon sets found in all other transcriptome assemblies | 294 | 535 | 1046 |
| Common exon set length (bp) (mean, IQR) | 677.75, 190-835 | 675.04, 189-831 | 667.28, 188-825 |
| Relative common exon set length (mean, IQR) | 0.98, 1-1 | 0.98, 1-1 | 0.97, 1-1 |
| Relative exon score | 0.9 | 0.894 | 0.879 |
| N missing exon sets inside transcript sets | 25978 | 27081 | 29373 |
| N missing exon sets outside transcript sets | 314 | 360 | 644 |
IQR = interquartile range
Figure 5. Exon set length distribution.
Figure 6. Exon set genomic distribution.
Exon set UpSet plot
Figure 7. Exon set UpSet plot.
Figure 8. Common exon set length distribution.
Figure 9. Common exon set relative length category
distribution.
Figure 10. Unique exon set length distribution.
Figure 11. Exon set pairwise completeness similarity.
Pairwise exon set Venn diagrams
Figure 12. Pairwise exon set Venn diagrams.
Figure 13. Exon set hierarchical clustering heatmap.
Table 4 Transcript set statistics.
| Parameter | d_melanogaster_bdgp6 | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 |
|---|---|---|---|---|---|---|---|
| N transcript sets | 12056 | 19948 | 22201 | 26626 | 12286 | 12441 | 12824 |
| Transcript set length (bp) (mean, IQR) | 7414.43, 1046.75-5999 | 3766.79, 315-2322 | 3236.22, 274-1839 | 2338.12, 227-1059 | 6935.85, 1079-5587.75 | 6831.46, 1052-5389 | 6504.71, 995-5018.5 |
| N isoforms per transcript set (mean, IQR) | 2.92, 1-3 | 1.38, 1-1 | 1.36, 1-1 | 1.31, 1-1 | 1.51, 1-1 | 1.49, 1-1 | 1.45, 1-1 |
| N, % transcript sets included in completeness analyses | 11951, 99.13% | 19913, 99.82% | 22152, 99.78% | 26417, 99.22% | 12278, 99.93% | 12436, 99.96% | 12810, 99.89% |
| N, % unique transcript sets | 134, 1.12% | 9, 0.05% | 7, 0.03% | 16, 0.06% | 3, 0.02% | 2, 0.02% | 6, 0.05% |
| Unique transcript set length (bp) (mean, IQR) | 835.46, 192-872 | 1065.56, 184-540 | 266.86, 166-199.5 | 219.69, 154.75-257.5 | 514.33, 506.5-525.5 | 362, 264-460 | 460.17, 163.5-502.75 |
| N missing transcript sets found in any transcriptome assembly | 1471 | 8518 | 10192 | 14651 | 4370 | 4502 | 4618 |
| N missing transcript sets found in all other transcriptome assemblies | 13 | 832 | 1534 | 5798 | 65 | 65 | 195 |
| Common transcript set length (bp) (mean, IQR) | 8620.99, 1395-7172 | 6682.68, 893-5155 | 6268.57, 749-4698 | 5241.27, 496-3729 | 8089.64, 1377-6614 | 8050.52, 1377-6525 | 7842.08, 1346-6306 |
| Relative common transcript set length (mean, IQR) | 1, 1-1 | 0.74, 0.55-0.96 | 0.68, 0.46-0.92 | 0.53, 0.28-0.8 | 0.96, 0.97-1 | 0.95, 0.96-1 | 0.93, 0.93-1 |
| Relative transcript score | 0.986 | 0.691 | 0.626 | 0.485 | 0.933 | 0.927 | 0.906 |
| Parameter | RSP_0.005_11_20 | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|---|
| N transcript sets | 12172 | 12265 | 12541 |
| Transcript set length (bp) (mean, IQR) | 7041.55, 1093-5692 | 6975.79, 1082-5590 | 6740.52, 1049-5276 |
| N isoforms per transcript set (mean, IQR) | 1.53, 1-1 | 1.52, 1-1 | 1.48, 1-1 |
| N, % transcript sets included in completeness analyses | 12167, 99.96% | 12262, 99.98% | 12531, 99.92% |
| N, % unique transcript sets | 2, 0.02% | 2, 0.02% | 11, 0.09% |
| Unique transcript set length (bp) (mean, IQR) | 1381, 1128.5-1633.5 | 248.5, 202.25-294.75 | 3023.91, 297.5-1128.5 |
| N missing transcript sets found in any transcriptome assembly | 4307 | 4436 | 4319 |
| N missing transcript sets found in all other transcriptome assemblies | 27 | 39 | 130 |
| Common transcript set length (bp) (mean, IQR) | 8154.03, 1386-6680 | 8122.05, 1379-6619 | 7979.94, 1371-6464 |
| Relative common transcript set length (mean, IQR) | 0.96, 0.98-1 | 0.96, 0.97-1 | 0.94, 0.95-1 |
| Relative transcript score | 0.939 | 0.933 | 0.921 |
IQR = interquartile range
Figure 14. Transcript set length distribution.
Figure 15. Number of isoforms per transcript set
category distribution.
Transcript set UpSet plot
Figure 16. Transcript set UpSet plot
Figure 17. Common transcript set length distribution.
Figure 18. Common transcript set relative length
category distribution.
Figure 19. Unique transcript set length distribution.
Figure 20. Transcript set pairwise completeness
similarity.
Pairwise transcript set Venn diagrams
Figure 21. Pairwise transcript set Venn diagrams.
Figure 22. Transcript set hierarchical clustering
heatmap.
Figure 23. Unique exon set position in non-origin
transcriptomes.
Figure 24. Missing exon set position.
Table 5. Annotation-based statistics.
| Parameter | d_melanogaster_bdgp6 | RSP_0.005_1_4 | RSP_0.01_1_4 | RSP_0.02_1_4 | RSP_0.005_5_10 | RSP_0.01_5_10 | RSP_0.02_5_10 |
|---|---|---|---|---|---|---|---|
| N, % exon sets included in completeness analyses | 64093, 100% | 63265, 100% | 63560, 100% | 62016, 100% | 60365, 100% | 60271, 100% | 59789, 100% |
| N, % matched transcriptome assembly exon sets (exon set precision) | 64067, 99.96% | 63210, 99.91% | 63521, 99.94% | 61966, 99.92% | 60341, 99.96% | 60240, 99.95% | 59768, 99.96% |
| N, % matched GTF exon sets (exon set recall) | 64067, 98.78% | 50950, 78.56% | 48427, 74.67% | 41823, 64.49% | 59176, 91.24% | 58870, 90.77% | 57811, 89.14% |
| Proprtion of covered transcriptome assembly exon sets (mean, IQR) | 0.988 | 0.707 | 0.665 | 0.565 | 0.885 | 0.877 | 0.855 |
| Annotation-based exon score | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 |
| N, % transcript sets included in completeness analyses | 11951, 99.13% | 19913, 99.82% | 22152, 99.78% | 26417, 99.22% | 12278, 99.93% | 12436, 99.96% | 12810, 99.89% |
| N, % matched transcriptome assembly transcript sets (transcript set precision) | 11924, 99.77% | 19876, 99.81% | 22111, 99.81% | 26381, 99.86% | 12255, 99.81% | 12410, 99.79% | 12785, 99.8% |
| N, % matched GTF transcript sets (transcript set recall) | 11864, 97.53% | 9988, 82.11% | 9229, 75.87% | 7235, 59.48% | 11544, 94.9% | 11520, 94.71% | 11467, 94.27% |
| Proprtion of covered transcriptome assembly transcript sets (mean, IQR) | 0.974 | 0.677 | 0.615 | 0.475 | 0.917 | 0.91 | 0.888 |
| Annotation-based transcript score | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 | 1, 1-1 |
| Parameter | RSP_0.005_11_20 | RSP_0.01_11_20 | RSP_0.02_11_20 |
|---|---|---|---|
| N, % exon sets included in completeness analyses | 60434, 100% | 60320, 100% | 60019, 100% |
| N, % matched transcriptome assembly exon sets (exon set precision) | 60406, 99.95% | 60304, 99.97% | 59979, 99.93% |
| N, % matched GTF exon sets (exon set recall) | 59430, 91.63% | 59187, 91.26% | 58463, 90.14% |
| Proprtion of covered transcriptome assembly exon sets (mean, IQR) | 0.891 | 0.885 | 0.87 |
| Annotation-based exon score | 1, 1-1 | 1, 1-1 | 1, 1-1 |
| N, % transcript sets included in completeness analyses | 12167, 99.96% | 12262, 99.98% | 12531, 99.92% |
| N, % matched transcriptome assembly transcript sets (transcript set precision) | 12146, 99.83% | 12243, 99.85% | 12495, 99.71% |
| N, % matched GTF transcript sets (transcript set recall) | 11555, 94.99% | 11570, 95.12% | 11546, 94.92% |
| Proprtion of covered transcriptome assembly transcript sets (mean, IQR) | 0.922 | 0.919 | 0.905 |
| Annotation-based transcript score | 1, 1-1 | 1, 1-1 | 1, 1-1 |
IQR = interquartile range
Figure 25. Proprtion of covered transcriptome exon sets
by a GTF exon set category distribution.
Annotation-based exon set UpSet plot
Figure 26. Annotation-based exon set UpSet plot.
Annotation-based pairwise exon set Venn diagrams
Figure 27. Annotation-based pairwise exon set Venn
diagrams.
Figure 28. Annotation-based exon set hierarchical
clustering heatmap.
Figure 29. Proportion of covered transcriptome
transcript sets by a GTF transcript set category distribution.
Annotation-based transcript set UpSet plot
Figure 30. Annotation-based transcript set UpSet plot.
Annotation-based pairwise transcript set Venn
diagrams
Figure 31. Annotation-based pairwise transcript set
Venn diagrams.
Figure 32. Annotation-based transcript set hierarchical
clustering heatmap.